I've been experiencing the Oblivion Gate weather sticking as well, below are my observations. I'm using All Natural version 1, OBSE 18, and Wrye Bash 287.
I think that during weather transitions city/interior/exterior loading causes the weather to reset to the previous weather, possibly canceling the transition. If the weather is in the process of transition from Oblivion Gate weather when this happens, the Oblivion Gate weather comes back and behaves like "normal" weather rather than being dependent on proximity to a gate. You then have to wait for it to run it's course like normal weather - although I've found continual city or interior/exterior loading can cause it to go away.
To test this I used a default All Natural ini and timescale of 30. I triggered Oblivion Gate weather and then ran to Cheydinhal. The weather had mostly transitioned back but I could still hear a little thunder. Upon entering Cheydinhal the Oblivion Gate weather was back in full force. It took hours of game time to go away if I just stood around (I would change my timescale to 1000 and it eventually went away) however entering and exiting buildings or the city could cause it to immediately disappear (no transition).
Having a lower timescale with the default All Natural ini exasperates this effect as you are more likely to cause city/interior/exterior loading during a transition (because transitions take longer) and weather lasts longer. I recommend lowering Transition Times for all weathers in the ini to match your timescale. I use this formula y/30=x where y is your timescale. Solve for x to get ideal Transition Time. As a work around to the Oblivion Gate weather consider reducing transition time even further. If you are already experiencing everlasting Gate weather, make sure you are not close to a gate, set your timescale to 1000, wait for it to go away. It should within minutes. Change back to your desired timescale.
To the authors of this mod are these recommendations sound? Please let me know if there is anything specific I can do to help.
That's a good anolysis and that has been my experience as well. I don't normally have the patience to wait around to determine when the gate weather actually stops - I either force it to clear or go inside a building, shop or whatever and then fast travel somewhere. I often wind up resting and by the time I'm done, it has cleared up. If I'm still outside, without entering a city, building or dungeon, then the gate weather clears up ok, but I think it should be instantaneous when you close a gate. However it usually hasn't fully cleared by the time I do a zone transition and it will reset to full force.